REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0052AL009_4 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0052  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0052 Cyanovirin-N, Nostoc ellipsosporum  
METHOD This prediction is based, in part, on a threading algorithm described in   
METHOD three publications:  
METHOD (i) "A polynomial-time algorithm for a class of protein threading  
METHOD problems", by Ying Xu and Edward C. Uberbacher, CABIOS (journal)   
METHOD Vol.12, No.6, 1996 pp.511-517  
METHOD (ii) "A New Method for Modeling and Solving the Protein Fold Recognition  
METHOD Problem", by Y. Xu, D. Xu, and E.C. Uberbacher, Proc. of RECOMB 98  
METHOD Second Annual Int'l Conf. on Computational Molecular Biology  
METHOD March 22-25, 1998, NEW York, NY, ACM Press, pp. 285-292  
METHOD (iii) "An Efficient Computational Method for Globally Optimal Threading",  
METHOD by Y. Xu, D. Xu, and E.C. Uberbacher, invited paper to appear in  
METHOD Journal of Computational Biology, 1998.  
METHOD  
METHOD  
METHOD The prediction is also based, in part, on a different threading algorithm  
METHOD described in the following publication:  
METHOD (iv) "A fast, reliable method for threading", by O.H. Crawford, submitted  
METHOD to Bioinformatics (journal)  
METHOD  
METHOD  
METHOD The energy model employed in the threading is based on improvements and   
METHOD extensions of the energy modeling described in Refs. (ii) and (iii)   
METHOD and in the following paper:  
METHOD (v) "Protein Fold Recognition at the Secondary Structure Level",  
METHOD by D. Xu, M.A. Unseren, Y. Xu, and E.C. Uberbacher, Submitted to  
METHOD Protein Science.  
METHOD   
METHOD   
METHOD Members of Oak Ridge National Laboratory's Computational Biosciences   
METHOD Section participating in CASP3  include (in alphabetical order):  
METHOD Oakley Crawford, J. Ralph Einstein, Frank W. Larimer, Richard Mural,   
METHOD Edward C. Uberbacher, Michael A. Unseren, Dong Xu, Ying Xu, and Ge Zhang  
MODEL 4  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 3cd4 
ATOM      1  N   PHE     4      18.060  10.939  76.182  1.00  0.00              
ATOM      2  CA  PHE     4      18.633  10.998  74.851  1.00  0.00              
ATOM      3  C   PHE     4      19.649  12.113  74.705  1.00  0.00              
ATOM      4  O   PHE     4      19.357  13.239  75.044  1.00  0.00              
ATOM      5  N   SER     5      20.831  11.877  74.140  1.00  0.00              
ATOM      6  CA  SER     5      21.765  12.968  73.958  1.00  0.00              
ATOM      7  C   SER     5      22.168  13.164  72.472  1.00  0.00              
ATOM      8  O   SER     5      22.514  12.240  71.727  1.00  0.00              
ATOM      9  N   GLN     6      22.002  14.387  71.960  1.00  0.00              
ATOM     10  CA  GLN     6      22.360  14.704  70.587  1.00  0.00              
ATOM     11  C   GLN     6      23.496  15.711  70.616  1.00  0.00              
ATOM     12  O   GLN     6      23.719  16.364  71.623  1.00  0.00              
ATOM     13  N   THR     7      24.315  15.798  69.579  1.00  0.00              
ATOM     14  CA  THR     7      25.366  16.791  69.612  1.00  0.00              
ATOM     15  C   THR     7      25.472  17.407  68.237  1.00  0.00              
ATOM     16  O   THR     7      25.375  16.690  67.246  1.00  0.00              
ATOM     17  N   CYS     8      25.599  18.729  68.132  1.00  0.00              
ATOM     18  CA  CYS     8      25.736  19.371  66.827  1.00  0.00              
ATOM     19  C   CYS     8      27.197  19.596  66.411  1.00  0.00              
ATOM     20  O   CYS     8      28.001  20.168  67.163  1.00  0.00              
ATOM     21  N   TYR     9      27.576  19.117  65.218  1.00  0.00              
ATOM     22  CA  TYR     9      28.930  19.307  64.759  1.00  0.00              
ATOM     23  C   TYR     9      28.990  20.607  64.002  1.00  0.00              
ATOM     24  O   TYR     9      28.148  20.858  63.193  1.00  0.00              
ATOM     25  N   THR    21      22.520  28.197  67.323  1.00  0.00              
ATOM     26  CA  THR    21      21.635  27.743  68.374  1.00  0.00              
ATOM     27  C   THR    21      20.740  26.644  67.809  1.00  0.00              
ATOM     28  O   THR    21      20.066  26.822  66.799  1.00  0.00              
ATOM     29  N   CYS    22      20.714  25.481  68.451  1.00  0.00              
ATOM     30  CA  CYS    22      19.937  24.361  67.964  1.00  0.00              
ATOM     31  C   CYS    22      18.620  24.216  68.696  1.00  0.00              
ATOM     32  O   CYS    22      18.540  24.481  69.896  1.00  0.00              
ATOM     33  N   GLU    23      17.548  23.768  68.058  1.00  0.00              
ATOM     34  CA  GLU    23      16.353  23.634  68.855  1.00  0.00              
ATOM     35  C   GLU    23      15.462  22.527  68.341  1.00  0.00              
ATOM     36  O   GLU    23      14.715  22.699  67.387  1.00  0.00              
ATOM     37  N   ASN    26      15.941  22.919  73.651  1.00  0.00              
ATOM     38  CA  ASN    26      16.862  23.697  72.810  1.00  0.00              
ATOM     39  C   ASN    26      18.185  23.997  73.502  1.00  0.00              
ATOM     40  O   ASN    26      18.222  24.334  74.680  1.00  0.00              
ATOM     41  N   GLY    27      19.304  23.936  72.793  1.00  0.00              
ATOM     42  CA  GLY    27      20.509  24.213  73.508  1.00  0.00              
ATOM     43  C   GLY    27      21.617  24.691  72.620  1.00  0.00              
ATOM     44  O   GLY    27      21.454  25.486  71.721  1.00  0.00              
ATOM     45  N   THR    31      25.351  20.665  72.641  1.00  0.00              
ATOM     46  CA  THR    31      24.862  19.371  73.183  1.00  0.00              
ATOM     47  C   THR    31      23.417  19.461  73.700  1.00  0.00              
ATOM     48  O   THR    31      23.034  20.341  74.439  1.00  0.00              
ATOM     49  N   SER    32      22.552  18.559  73.308  1.00  0.00              
ATOM     50  CA  SER    32      21.194  18.577  73.804  1.00  0.00              
ATOM     51  C   SER    32      20.908  17.294  74.586  1.00  0.00              
ATOM     52  O   SER    32      21.451  16.200  74.329  1.00  0.00              
ATOM     53  N   SER    33      19.995  17.368  75.546  1.00  0.00              
ATOM     54  CA  SER    33      19.704  16.152  76.243  1.00  0.00              
ATOM     55  C   SER    33      18.317  16.081  76.775  1.00  0.00              
ATOM     56  O   SER    33      17.738  17.041  77.215  1.00  0.00              
ATOM     57  N   ILE    34      17.749  14.915  76.623  1.00  0.00              
ATOM     58  CA  ILE    34      16.421  14.649  77.102  1.00  0.00              
ATOM     59  C   ILE    34      16.530  13.596  78.209  1.00  0.00              
ATOM     60  O   ILE    34      16.592  12.402  77.952  1.00  0.00              
ATOM     61  N   GLY    45       9.304   8.143  67.643  1.00  0.00              
ATOM     62  CA  GLY    45       8.792   8.858  66.500  1.00  0.00              
ATOM     63  C   GLY    45       9.882   9.433  65.628  1.00  0.00              
ATOM     64  O   GLY    45      10.888   8.784  65.332  1.00  0.00              
ATOM     65  N   SER    46       9.657  10.646  65.145  1.00  0.00              
ATOM     66  CA  SER    46      10.639  11.279  64.313  1.00  0.00              
ATOM     67  C   SER    46      10.661  12.730  64.721  1.00  0.00              
ATOM     68  O   SER    46       9.627  13.379  64.695  1.00  0.00              
ATOM     69  N   GLU    56      15.237  18.750  64.461  1.00  0.00              
ATOM     70  CA  GLU    56      16.058  19.742  65.064  1.00  0.00              
ATOM     71  C   GLU    56      16.265  20.866  64.080  1.00  0.00              
ATOM     72  O   GLU    56      16.174  20.710  62.850  1.00  0.00              
ATOM     73  N   THR    57      16.541  22.024  64.647  1.00  0.00              
ATOM     74  CA  THR    57      16.707  23.204  63.863  1.00  0.00              
ATOM     75  C   THR    57      18.031  23.862  64.173  1.00  0.00              
ATOM     76  O   THR    57      18.358  24.051  65.334  1.00  0.00              
ATOM     77  N   CYS    58      18.872  24.075  63.166  1.00  0.00              
ATOM     78  CA  CYS    58      20.087  24.814  63.430  1.00  0.00              
ATOM     79  C   CYS    58      19.881  26.171  62.774  1.00  0.00              
ATOM     80  O   CYS    58      19.319  26.260  61.693  1.00  0.00              
ATOM     81  N   ARG    59      20.185  27.263  63.460  1.00  0.00              
ATOM     82  CA  ARG    59      19.955  28.580  62.890  1.00  0.00              
ATOM     83  C   ARG    59      21.187  29.461  62.983  1.00  0.00              
ATOM     84  O   ARG    59      21.645  29.745  64.080  1.00  0.00              
ATOM     85  N   ASN    60      21.739  29.847  61.827  1.00  0.00              
ATOM     86  CA  ASN    60      22.912  30.696  61.731  1.00  0.00              
ATOM     87  C   ASN    60      22.593  31.809  60.756  1.00  0.00              
ATOM     88  O   ASN    60      22.159  31.560  59.622  1.00  0.00              
ATOM     89  N   ALA    71      19.604  32.332  58.366  1.00  0.00              
ATOM     90  CA  ALA    71      19.471  31.023  57.746  1.00  0.00              
ATOM     91  C   ALA    71      19.155  29.886  58.702  1.00  0.00              
ATOM     92  O   ALA    71      19.281  29.996  59.922  1.00  0.00              
ATOM     93  N   GLU    72      18.817  28.730  58.123  1.00  0.00              
ATOM     94  CA  GLU    72      18.520  27.563  58.916  1.00  0.00              
ATOM     95  C   GLU    72      18.425  26.251  58.143  1.00  0.00              
ATOM     96  O   GLU    72      18.007  26.165  57.002  1.00  0.00              
ATOM     97  N   CYS    73      18.917  25.198  58.777  1.00  0.00              
ATOM     98  CA  CYS    73      18.915  23.854  58.225  1.00  0.00              
ATOM     99  C   CYS    73      18.020  22.958  59.096  1.00  0.00              
ATOM    100  O   CYS    73      17.652  23.312  60.206  1.00  0.00              
ATOM    101  N   LYS    74      17.616  21.788  58.665  1.00  0.00              
ATOM    102  CA  LYS    74      16.714  21.065  59.522  1.00  0.00              
ATOM    103  C   LYS    74      17.015  19.575  59.521  1.00  0.00              
ATOM    104  O   LYS    74      17.076  18.936  58.474  1.00  0.00              
ATOM    105  N   THR    75      17.213  18.953  60.684  1.00  0.00              
ATOM    106  CA  THR    75      17.511  17.528  60.650  1.00  0.00              
ATOM    107  C   THR    75      16.356  16.752  61.222  1.00  0.00              
ATOM    108  O   THR    75      15.723  17.199  62.157  1.00  0.00              
ATOM    109  N   ASN    86      14.642   9.758  63.533  1.00  0.00              
ATOM    110  CA  ASN    86      13.570   9.008  64.134  1.00  0.00              
ATOM    111  C   ASN    86      14.157   8.246  65.302  1.00  0.00              
ATOM    112  O   ASN    86      15.181   7.564  65.159  1.00  0.00              
ATOM    113  N   LEU    87      13.551   8.443  66.485  1.00  0.00              
ATOM    114  CA  LEU    87      13.983   7.835  67.748  1.00  0.00              
ATOM    115  C   LEU    87      13.070   6.673  68.168  1.00  0.00              
ATOM    116  O   LEU    87      11.844   6.786  68.064  1.00  0.00              
ATOM    117  N   ILE    91      11.546   4.565  71.250  1.00  0.00              
ATOM    118  CA  ILE    91      11.592   4.188  72.653  1.00  0.00              
ATOM    119  C   ILE    91      10.811   2.912  72.876  1.00  0.00              
ATOM    120  O   ILE    91       9.663   2.784  72.433  1.00  0.00              
ATOM    121  N   ALA    92      11.421   1.925  73.536  1.00  0.00              
ATOM    122  CA  ALA    92      10.689   0.688  73.722  1.00  0.00              
ATOM    123  C   ALA    92      10.398   0.391  75.187  1.00  0.00              
ATOM    124  O   ALA    92      11.178   0.727  76.098  1.00  0.00              
END
